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Ghasemian E, Faal N, Pickering H, Sillah A, Breuer J, Bailey RL, Mabey D, Holland MJ. Genomic insights into local-scale evolution of ocular Chlamydia trachomatis strains within and between individuals in Gambian trachoma-endemic villages. Microb Genom 2024; 10:001210. [PMID: 38445851 PMCID: PMC10999739 DOI: 10.1099/mgen.0.001210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 02/12/2024] [Indexed: 03/07/2024] Open
Abstract
Trachoma, a neglected tropical disease caused by Chlamydia trachomatis (Ct) serovars A-C, is the leading infectious cause of blindness worldwide. Africa bears the highest burden, accounting for over 86 % of global trachoma cases. We investigated Ct serovar A (SvA) and B (SvB) whole genome sequences prior to the induction of mass antibiotic drug administration in The Gambia. Here, we explore the factors contributing to Ct strain diversification and the implications for Ct evolution within the context of ocular infection. A cohort study in 2002-2003 collected ocular swabs across nine Gambian villages during a 6 month follow-up study. To explore the genetic diversity of Ct within and between individuals, we conducted whole-genome sequencing (WGS) on a limited number (n=43) of Ct-positive samples with an omcB load ≥10 from four villages. WGS was performed using target enrichment with SureSelect and Illumina paired-end sequencing. Out of 43 WGS samples, 41 provided sufficient quality for further analysis. ompA analysis revealed that 11 samples had highest identity to ompA from strain A/HAR13 (NC_007429) and 30 had highest identity to ompA from strain B/Jali20 (NC_012686). While SvB genome sequences formed two distinct village-driven subclades, the heterogeneity of SvA sequences led to the formation of many individual branches within the Gambian SvA subclade. Comparing the Gambian SvA and SvB sequences with their reference strains, Ct A/HAR13 and Ct B/Jali20, indicated an single nucleotide polymorphism accumulation rate of 2.4×10-5 per site per year for the Gambian SvA and 1.3×10-5 per site per year for SvB variants (P<0.0001). Variant calling resulted in a total of 1371 single nucleotide variants (SNVs) with a frequency >25 % in SvA sequences, and 438 SNVs in SvB sequences. Of note, in SvA variants, highest evolutionary pressure was recorded on genes responsible for host cell modulation and intracellular survival mechanisms, whereas in SvB variants this pressure was mainly on genes essential for DNA replication/repair mechanisms and protein synthesis. A comparison of the sequences between observed separate infection events (4-20 weeks between infections) suggested that the majority of the variations accumulated in genes responsible for host-pathogen interaction such as CTA_0166 (phospholipase D-like protein), CTA_0498 (TarP) and CTA_0948 (deubiquitinase). This comparison of Ct SvA and SvB variants within a trachoma endemic population focused on their local evolutionary adaptation. We found a different variation accumulation pattern in the Gambian SvA chromosomal genes compared with SvB, hinting at the potential of Ct serovar-specific variation in diversification and evolutionary fitness. These findings may have implications for optimizing trachoma control and prevention strategies.
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Affiliation(s)
- Ehsan Ghasemian
- Department of Clinical Research, London School of Hygiene & Tropical Medicine, London, UK
| | - Nkoyo Faal
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Banjul, Gambia
| | - Harry Pickering
- Department of Clinical Research, London School of Hygiene & Tropical Medicine, London, UK
| | - Ansumana Sillah
- National Eye Health Programme, Ministry of Health, Kanifing, Gambia
| | - Judith Breuer
- Division of Infection and Immunity, University College London, London, UK
| | - Robin L. Bailey
- Department of Clinical Research, London School of Hygiene & Tropical Medicine, London, UK
| | - David Mabey
- Department of Clinical Research, London School of Hygiene & Tropical Medicine, London, UK
| | - Martin J. Holland
- Department of Clinical Research, London School of Hygiene & Tropical Medicine, London, UK
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Nysten J, Sofras D, Van Dijck P. One species, many faces: The underappreciated importance of strain diversity. PLoS Pathog 2024; 20:e1011931. [PMID: 38271302 PMCID: PMC10810500 DOI: 10.1371/journal.ppat.1011931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2024] Open
Affiliation(s)
- Jana Nysten
- Laboratory of Molecular Cell Biology, Department of Biology, Institute of Botany and Microbiology, KU Leuven, Leuven, Belgium
| | - Dimitrios Sofras
- Laboratory of Molecular Cell Biology, Department of Biology, Institute of Botany and Microbiology, KU Leuven, Leuven, Belgium
| | - Patrick Van Dijck
- Laboratory of Molecular Cell Biology, Department of Biology, Institute of Botany and Microbiology, KU Leuven, Leuven, Belgium
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Shikov AE, Savina IA, Nizhnikov AA, Antonets KS. Recombination in Bacterial Genomes: Evolutionary Trends. Toxins (Basel) 2023; 15:568. [PMID: 37755994 PMCID: PMC10534446 DOI: 10.3390/toxins15090568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 09/02/2023] [Accepted: 09/07/2023] [Indexed: 09/28/2023] Open
Abstract
Bacterial organisms have undergone homologous recombination (HR) and horizontal gene transfer (HGT) multiple times during their history. These processes could increase fitness to new environments, cause specialization, the emergence of new species, and changes in virulence. Therefore, comprehensive knowledge of the impact and intensity of genetic exchanges and the location of recombination hotspots on the genome is necessary for understanding the dynamics of adaptation to various conditions. To this end, we aimed to characterize the functional impact and genomic context of computationally detected recombination events by analyzing genomic studies of any bacterial species, for which events have been detected in the last 30 years. Genomic loci where the transfer of DNA was detected pertained to mobile genetic elements (MGEs) housing genes that code for proteins engaged in distinct cellular processes, such as secretion systems, toxins, infection effectors, biosynthesis enzymes, etc. We found that all inferences fall into three main lifestyle categories, namely, ecological diversification, pathogenesis, and symbiosis. The latter primarily exhibits ancestral events, thus, possibly indicating that adaptation appears to be governed by similar recombination-dependent mechanisms.
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Affiliation(s)
- Anton E. Shikov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia; (A.E.S.); (I.A.S.); (A.A.N.)
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia
| | - Iuliia A. Savina
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia; (A.E.S.); (I.A.S.); (A.A.N.)
| | - Anton A. Nizhnikov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia; (A.E.S.); (I.A.S.); (A.A.N.)
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia
| | - Kirill S. Antonets
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia; (A.E.S.); (I.A.S.); (A.A.N.)
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia
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Joseph SJ, Bommana S, Ziklo N, Kama M, Dean D, Read TD. Patterns of within-host spread of Chlamydia trachomatis between vagina, endocervix and rectum revealed by comparative genomic analysis. Front Microbiol 2023; 14:1154664. [PMID: 37056744 PMCID: PMC10086254 DOI: 10.3389/fmicb.2023.1154664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 03/06/2023] [Indexed: 03/30/2023] Open
Abstract
Introduction Chlamydia trachomatis, a gram-negative obligate intracellular bacterium, commonly causes sexually transmitted infections (STIs). Little is known about C. trachomatis transmission within the host, which is important for understanding disease epidemiology and progression. Methods We used RNA-bait enrichment and whole-genome sequencing to compare rectal, vaginal and endocervical samples collected at the same time from 26 study participants who attended Fijian Ministry of Health and Medical Services clinics and tested positive for C. trachomatis at each anatomic site. Results The 78 C. trachomatis genomes from participants resolved into two major clades of the C. trachomatis phylogeny (the "prevalent urogenital and anorectal" clade and "non-prevalent urogenital and anorectal" clade). For 21 participants, genome sequences were almost identical in each anatomic site. For the other five participants, two distinct C. trachomatis strains were present in different sites; in two cases, the vaginal sample was a mixture of strains. Discussion The absence of large numbers of fixed SNPs between C. trachomatis genomes within many of the participants could indicate recent acquisition of infection prior to the clinic visit without sufficient time to accumulate significant genetic variation in different body sites. This model suggests that many C. trachomatis infections may be resolved relatively quickly in the Fijian population, possibly reflecting common prescription or over-the-counter antibiotics usage.
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Affiliation(s)
- Sandeep J. Joseph
- Division of STD Prevention, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Sankhya Bommana
- Department of Pediatrics, University of California, San Francisco, Oakland, CA, United States
| | - Noa Ziklo
- Department of Pediatrics, University of California, San Francisco, Oakland, CA, United States
| | - Mike Kama
- Ministry of Health and Medical Services, Suva, Fiji
| | - Deborah Dean
- Department of Pediatrics, University of California, San Francisco, Oakland, CA, United States
- Department of Medicine, University of California, San Francisco, San Francisco, CA, United States
- Department of Bioengineering, Joint Graduate Program, University of California, San Francisco, San Francisco, CA, United States
- Department of Bioengineering, Joint Graduate Program, University of California, Berkeley, Berkeley, CA, United States
| | - Timothy D. Read
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, United States
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Joseph SJ, Bommana S, Ziklo N, Kama M, Dean D, Read TD. Patterns of within-host spread of Chlamydia trachomatis between vagina, endocervix and rectum revealed by comparative genomic analysis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.25.525576. [PMID: 36747780 PMCID: PMC9901013 DOI: 10.1101/2023.01.25.525576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Chlamydia trachomatis , a gram-negative obligate intracellular bacterium, commonly causes sexually transmitted infections (STIs). Little is known about C. trachomatis transmission within the host, which is important for understanding disease epidemiology and progression. We used RNA-bait enrichment and whole-genome sequencing to compare rectal, vaginal and endocervical samples collected at the same time from 26 study participants who attended Fijian Ministry of Health and Medical Services clinics and tested positive for C. trachomatis at each anatomic site. The 78 C. trachomatis genomes from participants were from two major clades of the C. trachomatis phylogeny (the "prevalent urogenital and anorecta"l clade and "non-prevalent urogenital and anorectal" clade). For 21 participants, genome sequences were almost identical in each anatomic site. For the other five participants, two distinct C. trachomatis strains were present in different sites; in two cases, the vaginal sample was a mixture of strains. The absence of large numbers of fixed SNPs between C. trachomatis strains within many of the participants could indicate recent acquisition of infection prior to the clinic visit without sufficient time to accumulate significant variation in the different body sites. This model suggests that many C. trachomatis infections may be resolved relatively quickly in the Fijian population, possibly reflecting common prescription or over-the-counter antibiotics usage. Importance Chlamydia trachomatis is a bacterial pathogen that causes millions of sexually transmitted infections (STIs) annually across the globe. Because C. trachomatis lives inside human cells, it has historically been hard to study. We know little about how the bacterium spreads between body sites. Here, samples from 26 study participants who had simultaneous infections in their vagina, rectum and endocervix were genetically analyzed using an improved method to extract C. trachomatis DNA directly from clinical samples for genome sequencing. By analyzing patterns of mutations in the genomes, we found that 21 participants shared very similar C. trachomatis strains in all three anatomic sites, suggesting recent infection and spread. For five participants two C. trachomatis strains were evident, indicating multiple infections. This study is significant in that improved enrichment methods for genome sequencing provides robust data to genetically trace patterns of C. trachomatis infection and transmission within an individual for epidemiologic and pathogenesis interrogations.
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Affiliation(s)
- Sandeep J. Joseph
- Division of STD Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Sankhya Bommana
- Department of Pediatrics, University of California San Francisco, Oakland, California, USA
| | - Noa Ziklo
- Department of Pediatrics, University of California San Francisco, Oakland, California, USA
| | - Mike Kama
- Ministry of Health and Medical Services, Suva, Fiji
| | - Deborah Dean
- Department of Pediatrics, University of California San Francisco, Oakland, California, USA,Department of Medicine, University of California San Francisco, San Francisco, California, USA,Department of Bioengineering, Joint Graduate Program, University of California San Francisco and University of California Berkeley, San Francisco, California, USA,Bixby Center for Global Reproductive Health, University of California San Francisco, San Francisco, California, USA,Benioff Center for Microbiome Medicine, University of California San Francisco, San Francisco, California, USA,Corresponding authors, contributed equally, DD: , TDR:
| | - Timothy D. Read
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA,Corresponding authors, contributed equally, DD: , TDR:
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Gravett RM, Marrazzo J. What’s Old Is New: the Evolution of Lymphogranuloma Venereum Proctitis in Persons Living with HIV. Curr Infect Dis Rep 2022. [DOI: 10.1007/s11908-022-00781-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Prophylactic Multi-Subunit Vaccine against Chlamydia trachomatis: In Vivo Evaluation in Mice. Vaccines (Basel) 2021; 9:vaccines9060609. [PMID: 34204170 PMCID: PMC8226540 DOI: 10.3390/vaccines9060609] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 05/31/2021] [Accepted: 06/03/2021] [Indexed: 01/08/2023] Open
Abstract
Chlamydia trachomatis is the most frequent sexually-transmitted disease-causing bacterium. Urogenital serovars of this intracellular pathogen lead to urethritis and cervicitis. Ascending infections result in pelvic inflammatory disease, salpingitis, and oophoritis. One of 200 urogenital infections leads to tubal infertility. Serovars A–C cause trachoma with visual impairment. There is an urgent need for a vaccine. We characterized a new five-component subunit vaccine in a mouse vaccination-lung challenge infection model. Four recombinant Pmp family-members and Ctad1 from C. trachomatis serovar E, all of which participate in adhesion and binding of chlamydial elementary bodies to host cells, were combined with the mucosal adjuvant cyclic-di-adenosine monophosphate. Intranasal application led to a high degree of cross-serovar protection against urogenital and ocular strains of C. trachomatis, which lasted at least five months. Critical evaluated parameters were body weight, clinical score, chlamydial load, a granulocyte marker and the cytokines IFN-γ/TNF-α in lung homogenate. Vaccine antigen-specific antibodies and a mixed Th1/Th2/Th17 T cell response with multi-functional CD4+ and CD8+ T cells correlate with protection. However, serum-transfer did not protect the recipients suggesting that circulating antibodies play only a minor role. In the long run, our new vaccine might help to prevent the feared consequences of human C. trachomatis infections.
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Tryptophan Operon Diversity Reveals Evolutionary Trends among Geographically Disparate Chlamydia trachomatis Ocular and Urogenital Strains Affecting Tryptophan Repressor and Synthase Function. mBio 2021; 12:mBio.00605-21. [PMID: 33975934 PMCID: PMC8262981 DOI: 10.1128/mbio.00605-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The obligate intracellular pathogen Chlamydia trachomatis (Ct) is the leading cause of bacterial sexually transmitted infections and blindness globally. To date, Ct urogenital strains are considered tryptophan prototrophs, utilizing indole for tryptophan synthesis within a closed-conformation tetramer comprised of two α (TrpA)- and two β (TrpB)-subunits. In contrast, ocular strains are auxotrophs due to mutations in TrpA, relying on host tryptophan pools for survival. It has been speculated that there is strong selective pressure for urogenital strains to maintain a functional operon. Here, we performed genetic, phylogenetic, and novel functional modeling analyses of 595 geographically diverse Ct ocular, urethral, vaginal, and rectal strains with complete operon sequences. We found that ocular and urogenital, but not lymphogranuloma venereum, TrpA-coding sequences were under positive selection. However, vaginal and urethral strains exhibited greater nucleotide diversity and a higher ratio of nonsynonymous to synonymous substitutions [Pi(a)/Pi(s)] than ocular strains, suggesting a more rapid evolution of beneficial mutations. We also identified nonsynonymous amino acid changes for an ocular isolate with a urogenital backbone in the intergenic region between TrpR and TrpB at the exact binding site for YtgR-the only known iron-dependent transcription factor in Chlamydia-indicating that selective pressure has disabled the response to fluctuating iron levels. In silico effects on protein stability, ligand-binding affinity, and tryptophan repressor (TrpR) affinity for single-stranded DNA (ssDNA) measured by calculating free energy changes (ΔΔG) between Ct reference and mutant tryptophan operon proteins were also analyzed. We found that tryptophan synthase function was likely suboptimal compared to other bacterial tryptophan prototrophs and that a diversity of urogenital strain mutations rendered the synthase nonfunctional or inefficient. The novel mutations identified here affected active sites in an orthosteric manner but also hindered α- and β-subunit allosteric interactions from distant sites, reducing efficiency of the tryptophan synthase. Importantly, strains with mutant proteins were inclined toward energy conservation by exhibiting an altered affinity for their respective ligands compared to reference strains, indicating greater fitness. This is not surprising as l-tryptophan is one of the most energetically costly amino acids to synthesize. Mutations in the tryptophan repressor gene (trpR) among urogenital strains were similarly detrimental to function. Our findings indicate that urogenital strains are evolving more rapidly than previously recognized with mutations that impact tryptophan operon function in a manner that is energetically beneficial, providing a novel host-pathogen evolutionary mechanism for intracellular survival.IMPORTANCE Chlamydia trachomatis (Ct) is a major global public health concern causing sexually transmitted and ocular infections affecting over 130 million and 260 million people, respectively. Sequelae include infertility, preterm birth, ectopic pregnancy, and blindness. Ct relies on available host tryptophan pools and/or substrates to synthesize tryptophan to survive. Urogenital strains synthesize tryptophan from indole using their intact tryptophan synthase (TS). Ocular strains contain a trpA frameshift mutation that encodes a truncated TrpA with loss of TS function. We found that TS function is likely suboptimal compared to other tryptophan prototrophs and that urogenital stains contain diverse mutations that render TS nonfunctional/inefficient, evolve more rapidly than previously recognized, and impact operon function in a manner that is energetically beneficial, providing an alternative host-pathogen evolutionary mechanism for intracellular survival. Our research has broad scientific appeal since our approach can be applied to other bacteria that may explain evolution/survival in host-pathogen interactions.
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Whole-Genome Enrichment and Sequencing of Chlamydia trachomatis Directly from Patient Clinical Vaginal and Rectal Swabs. mSphere 2021; 6:6/2/e01302-20. [PMID: 33658279 PMCID: PMC8546720 DOI: 10.1128/msphere.01302-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Chlamydia trachomatis, an obligately intracellular bacterium, is the most prevalent cause of bacterial sexually transmitted infections (STIs) worldwide. Numbers of U.S. infections of the urogenital tract and rectum have increased annually. Because C. trachomatis is not easily cultured, comparative genomic studies are limited, restricting our understanding of strain diversity and emergence among populations globally. While Agilent SureSelectXT target enrichment RNA bait libraries have been developed for whole-genome enrichment and sequencing of C. trachomatis directly from clinical urine, vaginal, conjunctival, and rectal samples, public access to these libraries is not available. We therefore designed an RNA bait library (34,795 120-mer probes based on 85 genomes, versus 33,619 probes using 74 genomes in a previous one) to augment organism sequencing from clinical samples that can be shared with the scientific community, enabling comparison studies. We describe the library and limit of detection for genome copy input, and we present results of 100% efficiency and high-resolution determination of recombination and identical genomes within vaginal-rectal specimen pairs in women. This workflow provides a robust approach for discerning genomic diversity and advancing our understanding of the molecular epidemiology of contemporary C. trachomatis STIs across sample types, geographic populations, sexual networks, and outbreaks associated with proctitis/proctocolitis among women and men who have sex with men.IMPORTANCE Chlamydia trachomatis is an obligate intracellular bacterium that is not easily cultured, which limits our understanding of urogenital and rectal C. trachomatis transmission and impact on morbidity. To provide a publicly available workflow for whole-genome target enrichment and sequencing of C. trachomatis directly from clinical urine, vaginal, conjunctival, and rectal specimens, we developed and report on an RNA bait library to enrich the organism from clinical samples for sequencing. We demonstrate an increased efficiency in the percentage of reads mapping to C. trachomatis and identified recombinant and identical C. trachomatis genomes in paired vaginal-rectal samples from women. Our workflow provides a robust genomic epidemiologic approach to advance our understanding of C. trachomatis strains causing ocular, urogenital, and rectal infections and to explore geo-sexual networks, outbreaks of colorectal infections among women and men who have sex with men, and the role of these strains in morbidity.
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Idahl A, Le Cornet C, González Maldonado S, Waterboer T, Bender N, Tjønneland A, Hansen L, Boutron-Ruault MC, Fournier A, Kvaskoff M, Boeing H, Trichopoulou A, Valanou E, Peppa E, Palli D, Agnoli C, Mattiello A, Tumino R, Sacerdote C, Onland-Moret NC, Gram IT, Weiderpass E, Quirós JR, Duell EJ, Sánchez MJ, Chirlaque MD, Barricarte A, Gil L, Brändstedt J, Riesbeck K, Lundin E, Khaw KT, Perez-Cornago A, Gunter MJ, Dossus L, Kaaks R, Fortner RT. Serologic markers of Chlamydia trachomatis and other sexually transmitted infections and subsequent ovarian cancer risk: Results from the EPIC cohort. Int J Cancer 2020; 147:2042-2052. [PMID: 32243586 DOI: 10.1002/ijc.32999] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 01/23/2020] [Accepted: 02/19/2020] [Indexed: 12/19/2022]
Abstract
A substantial proportion of epithelial ovarian cancer (EOC) arises in the fallopian tube and other epithelia of the upper genital tract; these epithelia may incur damage and neoplastic transformation after sexually transmitted infections (STI) and pelvic inflammatory disease. We investigated the hypothesis that past STI infection, particularly Chlamydia trachomatis, is associated with higher EOC risk in a nested case-control study within the European Prospective Investigation into Cancer and Nutrition (EPIC) cohort including 791 cases and 1669 matched controls. Serum antibodies against C. trachomatis, Mycoplasma genitalium, herpes simplex virus type 2 (HSV-2) and human papillomavirus (HPV) 16, 18 and 45 were assessed using multiplex fluorescent bead-based serology. Conditional logistic regression was used to estimate relative risks (RR) and 95% confidence intervals (CI) comparing women with positive vs. negative serology. A total of 40% of the study population was seropositive to at least one STI. Positive serology to C. trachomatis Pgp3 antibodies was not associated with EOC risk overall, but with higher risk of the mucinous histotype (RR = 2.30 [95% CI = 1.22-4.32]). Positive serology for chlamydia heat shock protein 60 (cHSP60-1) was associated with higher risk of EOC overall (1.36 [1.13-1.64]) and with the serous subtype (1.44 [1.12-1.85]). None of the other evaluated STIs were associated with EOC risk overall; however, HSV-2 was associated with higher risk of endometrioid EOC (2.35 [1.24-4.43]). The findings of our study suggest a potential role of C. trachomatis in the carcinogenesis of serous and mucinous EOC, while HSV-2 might promote the development of endometrioid disease.
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Affiliation(s)
- Annika Idahl
- Department of Clinical Sciences, Obstetrics and Gynecology, Umeå University, Umeå, Sweden
| | - Charlotte Le Cornet
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Tim Waterboer
- Infections and Cancer Epidemiology, Infection, Inflammation and Cancer Program, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Noemi Bender
- Infections and Cancer Epidemiology, Infection, Inflammation and Cancer Program, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Anne Tjønneland
- Danish Cancer Society Research Center, Diet, Genes and Environment (DGE), Copenhagen, Germany
| | - Louise Hansen
- Danish Cancer Society Research Center, Diet, Genes and Environment (DGE), Copenhagen, Germany
| | - Marie-Christine Boutron-Ruault
- CESP, Faculté de Médecine, Université Paris-Sud, UVSQ, INSERM, Université Paris-Saclay, Villejuif, France
- Gustave Roussy, Villejuif, France
| | - Agnès Fournier
- CESP, Faculté de Médecine, Université Paris-Sud, UVSQ, INSERM, Université Paris-Saclay, Villejuif, France
- Gustave Roussy, Villejuif, France
| | - Marina Kvaskoff
- CESP, Faculté de Médecine, Université Paris-Sud, UVSQ, INSERM, Université Paris-Saclay, Villejuif, France
- Gustave Roussy, Villejuif, France
| | - Heiner Boeing
- Department of Epidemiology, German Institute of Human Nutrition (DIfE) Potsdam-Rehbrücke, Nuthetal, Germany
| | | | | | | | - Domenico Palli
- Institute for Cancer Research, Prevention and Clinical Network - ISPRO, Cancer Risk Factors and Life-Style Epidemiology Unit, Florence, Italy
| | - Claudia Agnoli
- Istituto Nazionale dei Tumori di Milano Via Venezian, Epidemiology and Prevention Unit Fondazione IRCCS, Milan, Italy
| | - Amalia Mattiello
- Dipartimento di Medicina Clinica e Chirurgia, Federico II university, Naples, Italy
| | - Rosario Tumino
- Cancer Registry and Histopathology Department, "Civic - M.P. Arezzo" Hospital, ASP, Ragusa, Italy
| | - Carlotta Sacerdote
- Unit of Cancer Epidemiology, Città Della Salute e Della Scienza University-Hospital and Center for Cancer Prevention (CPO), Turin, Italy
| | - N Charlotte Onland-Moret
- Julius Center for Health Sciences and Primary Care, UMC Utrecht, YOUth onderzoek - Universiteit Utrecht, Utrecht, The Netherlands
| | - Inger T Gram
- Faculty of Health Sciences, Department of Community Medicine, University of Tromsø, The Arctic University of Norway, Tromsø, Norway
| | | | - Jose R Quirós
- J.S. Información Sanitaria, Dirección General de Salud Pública, Consejería de Sanidad, Oviedo, Spain
| | - Eric J Duell
- Unit of Nutrition and Cancer, Cancer Epidemiology Research Program, Catalan Institute of Oncology (ICO-IDIBELL), Barcelona, Spain
| | - Maria-Jose Sánchez
- Escuela Andaluza de Salud Pública, Instituto de Investigación Biosanitaria ibs.GRANADA. Hospitales Universitarios de Granada/Universidad de Granada, Granada, Spain
- CIBER in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Maria-Dolores Chirlaque
- CIBER in Epidemiology and Public Health (CIBERESP), Madrid, Spain
- Department of Epidemiology, Regional Health Council, IMIB-Arrixaca, Murcia, Spain
- Department of Health and Social Sciences, Universidad de Murcia, Murcia, Spain
| | - Aurelio Barricarte
- CIBER in Epidemiology and Public Health (CIBERESP), Madrid, Spain
- Navarra Public Health Institute, Pamplona, Spain
- Navarra Institute for Health Research (IdiSNA) Pamplona, Spain
| | - Leire Gil
- Public Health Division of Gipuzkoa, Research institute of BioDonostia, San Sebastian, Spain
| | - Jenny Brändstedt
- Department of Clinical Sciences, Lund University, Division of Surgery, Skåne University Hospital, Lund, Sweden
- Division of Surgery, Skåne University Hospital, Lund, Sweden
| | - Kristian Riesbeck
- Clinical Microbiology, Department of Translational Medicine, Lund University, Malmö, Sweden
| | - Eva Lundin
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
| | - Kay-Tee Khaw
- Department of Public Health and Primary Care, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Aurora Perez-Cornago
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Marc J Gunter
- International Agency for Research on Cancer, Lyon, France
| | - Laure Dossus
- International Agency for Research on Cancer, Lyon, France
| | - Rudolf Kaaks
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Renée T Fortner
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
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11
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Discovering the indigenous microbial communities associated with the natural fermentation of sap from the cider gum Eucalyptus gunnii. Sci Rep 2020; 10:14716. [PMID: 32895409 PMCID: PMC7477236 DOI: 10.1038/s41598-020-71663-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 08/19/2020] [Indexed: 12/13/2022] Open
Abstract
Over the course of human history and in most societies, fermented beverages have had a unique economic and cultural importance. Before the arrival of the first Europeans in Australia, Aboriginal people reportedly produced several fermented drinks including mangaitch from flowering cones of Banksia and way-a-linah from Eucalyptus tree sap. In the case of more familiar fermented beverages, numerous microorganisms, including fungi, yeast and bacteria, present on the surface of fruits and grains are responsible for the conversion of the sugars in these materials into ethanol. Here we describe native microbial communities associated with the spontaneous fermentation of sap from the cider gum Eucalyptus gunnii, a Eucalyptus tree native to the remote Central Plateau of Tasmania. Amplicon-based phylotyping showed numerous microbial species in cider gum samples, with fungal species differing greatly to those associated with winemaking. Phylotyping also revealed several fungal sequences which do not match known fungal genomes suggesting novel yeast species. These findings highlight the vast microbial diversity associated with the Australian Eucalyptus gunnii and the native alcoholic beverage way-a-linah.
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12
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Van Rossum T, Ferretti P, Maistrenko OM, Bork P. Diversity within species: interpreting strains in microbiomes. Nat Rev Microbiol 2020; 18:491-506. [PMID: 32499497 PMCID: PMC7610499 DOI: 10.1038/s41579-020-0368-1] [Citation(s) in RCA: 172] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/09/2020] [Indexed: 02/06/2023]
Abstract
Studying within-species variation has traditionally been limited to culturable bacterial isolates and low-resolution microbial community fingerprinting. Metagenomic sequencing and technical advances have enabled culture-free, high-resolution strain and subspecies analyses at high throughput and in complex environments. This holds great scientific promise but has also led to an overwhelming number of methods and terms to describe infraspecific variation. This Review aims to clarify these advances by focusing on the diversity within bacterial and archaeal species in the context of microbiomics. We cover foundational microevolutionary concepts relevant to population genetics and summarize how within-species variation can be studied and stratified directly within microbial communities with a focus on metagenomics. Finally, we describe how common applications of within-species variation can be achieved using metagenomic data. We aim to guide the selection of appropriate terms and analytical approaches to facilitate researchers in benefiting from the increasing availability of large, high-resolution microbiome genetic sequencing data.
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Affiliation(s)
- Thea Van Rossum
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Pamela Ferretti
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Oleksandr M Maistrenko
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Peer Bork
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany.
- Max Delbrück Centre for Molecular Medicine, Berlin, Germany.
- Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, Heidelberg, Germany.
- Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany.
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13
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Lymphoganuloma venereum in the Western world, 15 years after its re-emergence: new perspectives and research priorities. Curr Opin Infect Dis 2020; 32:43-50. [PMID: 30507675 DOI: 10.1097/qco.0000000000000519] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
PURPOSE OF REVIEW Lymphogranuloma venereum (LGV) is a serious sexually transmitted infection caused by Chlamydia trachomatis. If left untreated LGV can cause irreversible late sequelae. LGV is endemic among a high-risk population of men who have sex with men (MSM), and largely reported in Western metropoles. RECENT FINDINGS Although the majority of LGV patients are HIV positive, in recent years the proportion of HIV-negative MSM with LGV is rising. This could indicate a shift toward lower risk populations. Apart from a few European countries, no proper LGV surveillance efforts have been implemented so far. Moreover, a considerable proportion of the infections are asymptomatic. As a result, the true magnitude of the LGV epidemic is underestimated.Depending on the stage and location of infection, LGV manifests in a variety of clinical presentations. Among MSM, anorectal infections are overreported as opposed to genital LGV infections in a ratio of 15 to 1, respectively. Therefore, other modes of transmission apart from anal sex are here discussed. SUMMARY To improve surveillance, cheaper and more practical screening methods are needed. Moreover, randomized clinical trials are needed to evaluate more simple treatment modalities as opposed to the currently recommended 3-week course of doxycycline.
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Thapa J, Watanabe T, Isoba M, Okubo T, Abe K, Minami K, Yamaguchi H. Chlamydia trachomatis isolated from cervicovaginal samples in Sapporo, Japan, reveals the circulation of genetically diverse strains. BMC Infect Dis 2020; 20:53. [PMID: 31948401 PMCID: PMC6966806 DOI: 10.1186/s12879-020-4780-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Accepted: 01/08/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND This study was conducted to understand the molecular epidemiology of circulating Chlamydia trachomatis (Ct) strains in Sapporo, Japan. METHODS A total of 713 endocervical samples collected from April 2016 to March 2019 were screened for Ct. The obtained Ct positive samples were analyzed by ompA genotyping and multilocus sequence analysis (MLSA). RESULTS Eighty-three (11.6%) samples were positive for Ct plasmid DNA. Sequence analysis of the ompA gene from the 61 positive cases revealed eight genotypes: F (40.9%), E (19.6%), D (14.7%), G (9.8%), H (6.5%), I (3.2%), K (3.2%), and J (1.6%). The globally dominant genotype E and F strains were highly conserved with 13 ompA genetic variants being detected, whereas genotype D strains were the most diverse. Genetic characterization of D strains revealed that D1 genetic variants may be potentially specific to Sapporo. MLSA revealed 13 unique sequence types (STs) including four novel STs from 53 positive samples, with the globally dominant STs 39 and 19 being predominant. STs 39, 34, and 21 were exclusively associated with genotypes E and F indicating their global dominance. Novel ST70 and ST30 were specifically associated with genotype D. CONCLUSION Our study has revealed the circulation of genetically diverse Ct strains in the women population of Sapporo, Japan. We suggest identifying a transmission network of those successful strains and implementing public health prevention strategies to control the spread of Ct in Sapporo.
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Affiliation(s)
- Jeewan Thapa
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, Nishi-5 Kita-12 Jo, Kita-ku, Sapporo, Hokkaido, 060-0812, Japan
| | - Takanori Watanabe
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, Nishi-5 Kita-12 Jo, Kita-ku, Sapporo, Hokkaido, 060-0812, Japan
| | - Mana Isoba
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, Nishi-5 Kita-12 Jo, Kita-ku, Sapporo, Hokkaido, 060-0812, Japan
| | - Torahiko Okubo
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, Nishi-5 Kita-12 Jo, Kita-ku, Sapporo, Hokkaido, 060-0812, Japan
| | - Kiyotake Abe
- Toho Obstetrics and Gynecology Hospital, Higashi-15, Kita-17 Jo, Higashi-ku, Sapporo, 065-0017, Japan
| | - Kunihiro Minami
- Toho Obstetrics and Gynecology Hospital, Higashi-15, Kita-17 Jo, Higashi-ku, Sapporo, 065-0017, Japan
| | - Hiroyuki Yamaguchi
- Department of Medical Laboratory Science, Faculty of Health Sciences, Hokkaido University, Nishi-5 Kita-12 Jo, Kita-ku, Sapporo, Hokkaido, 060-0812, Japan.
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15
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An Asymptomatic Patient with Fatal Infertility Carried a Swedish Strain of Chlamydia trachomatis with Additional Deletion in The Plasmid orf1 that Belonged to A Different MLST Sequence Type. Microorganisms 2019; 7:microorganisms7070187. [PMID: 31261812 PMCID: PMC6681046 DOI: 10.3390/microorganisms7070187] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 06/20/2019] [Accepted: 06/25/2019] [Indexed: 01/31/2023] Open
Abstract
Here, we present the first case of asymptomatic genital Chlamydial infection caused by the new emerging Chlamydia trachomatis (C.t.) ST13 strain genovar E, which has a double deletion of 377 bp and 17 bp in orf1 gene of the cryptic plasmid (ddCT). This case occurred in an infertile patient (case-patient) with a detectable level of Chlamydial antibodies and a spermatozoa deficiency known as azoospermia. Additionally, the ddCT strain showed the presence of a duplication of 44 bp in the plasmid orf3 and SNP in orf4, which were known as the typical characteristics of the Swedish variant of C.t. (nvCT) genovar E. Multilocus sequence typing (MLST) determined a significant difference between ddCT and nvCT in four alleles (oppA, hfiX, gitA and enoA). Both ddCT and nvCT were assigned to different genetic lineages and could be allocated to two different non-overlapping clonal complexes. Furthermore, ddCT demonstrated a considerable difference among 4–5 alleles in comparison with other C.t. strains of genovar E of ST4, ST8, ST12, and ST94, including the founder of a single relevant cluster, wtCT E/SW3 (Swedish genetic lineage). In contrast to other genovar E strains, ddCT had identical alleles with seven out of seven loci found in ST13 strains of genovars D and G, including the founder for this clonal group, D/UW-3/CX, and six out of seven loci found in its derivatives, such as ST6, ST10, and ST95 of genovars G and H. Nevertheless, MSTree V2 showed that ddCT and nvCT could have a common early ancestor, which is a parental C.t. G/9301 strain of ST9. A significant difference between ddCT and nvCT of genovar D (nvCT-D) that was recently found in Mexico was also determined as: (i) ddCT belonged to genovar E but not to genovar D; (ii) ddCT had a 44 bp duplication within the orf3 of the plasmid typical for nvCT; (iii) ddCT possessed an additional 17 bp deletion in the orf1. In conclusion, improved case management should include the clinical physician’s awareness of the need to enhance molecular screening of asymptomatic Chlamydia patients. Such molecular diagnostics might be essential to significantly reducing the global burden of Chlamydial infection on international public health.
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de Vries HJC, de Barbeyrac B, de Vrieze NHN, Viset JD, White JA, Vall-Mayans M, Unemo M. 2019 European guideline on the management of lymphogranuloma venereum. J Eur Acad Dermatol Venereol 2019; 33:1821-1828. [PMID: 31243838 DOI: 10.1111/jdv.15729] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 05/17/2019] [Indexed: 11/26/2022]
Abstract
New or important issues in this updated version of the 2013 European guideline on the management of lymphogranuloma venereum (LGV): EPIDEMIOLOGY: Lymphogranuloma venereum continues to be endemic among European men who have sex with men (MSM) since 2003. Lymphogranuloma venereum infections in heterosexuals are extremely rare in Europe, and there is no evidence of transmission of LGV in the European heterosexual population. AETIOLOGY AND TRANSMISSION Chlamydia trachomatis serovars/genovars L2b and L2 are the causative strains in the majority of cases in Europe. CLINICAL FEATURES Among MSM, about 25% of the anorectal LGV infections are asymptomatic. Genital infections among MSM are rare; the ratio of genital vs. anorectal LGV infections is 1 in 15. DIAGNOSIS To diagnose LGV, a sample tested C. trachomatis positive with a commercial nucleic acid amplification test (NAAT) platform should be confirmed with an LGV discriminatory NAAT. TREATMENT Doxycycline 100 mg twice a day orally for 21 days is the recommended treatment for LGV. This same treatment is recommended also in asymptomatic patients and contacts of LGV patients. If another regimen is used, a test of cure (TOC) must be performed.
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Affiliation(s)
- H J C de Vries
- STI Outpatient Clinic, Infectious Diseases Department, Public Health Service Amsterdam, Amsterdam, The Netherlands.,Department of Dermatology, Amsterdam Institute for Infection and Immunity (AI&II), Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - B de Barbeyrac
- Mycoplasmal and Chlamydial Infections in Humans, University of Bordeaux, Bordeaux, France.,Mycoplasmal and Chlamydial Infections in Humans, INRA, Bordeaux, France.,Centre Hospitalier Universitaire de Bordeaux, Laboratoire de Bacteriologie, French National Reference Center for Bacterial STIs, Bordeaux, France
| | - N H N de Vrieze
- Department of Dermatology, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - J D Viset
- Department of Dermatology, Amsterdam Institute for Infection and Immunity (AI&II), Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - J A White
- Department of Genitourinary Medicine, Western Health & Social Care Trust, Londonderry, UK
| | - M Vall-Mayans
- STI Unit Vall d'Hebron-Drassanes, Department of Infectious Diseases, Hospital Vall d'Hebron, Barcelona, Spain
| | - M Unemo
- WHO Collaborating Centre for Gonorrhoea and Other Sexually Transmitted Infections, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
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17
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Urogenital Chlamydia trachomatis multilocus sequence types and genovar distribution in chlamydia infected patients in a multi-ethnic region of Saratov, Russia. PLoS One 2018; 13:e0195386. [PMID: 29641543 PMCID: PMC5895025 DOI: 10.1371/journal.pone.0195386] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Accepted: 03/21/2018] [Indexed: 11/19/2022] Open
Abstract
Background This is the first report to characterize the prevalence and genovar distribution of genital chlamydial infections among random heterosexual patients in the multi-ethnic Saratov Region, located in Southeast Russia. Methods Sixty-one clinical samples (cervical or urethral swabs) collected from a random cohort of 856 patients (7.1%) were C. trachomatis (CT) positive in commercial nucleic acid amplification tests (NAATs) and duplex TaqMan PCRs. Results Sequence analysis of the VDII region of the ompA gene revealed seven genovars of C. trachomatis in PCR-positive patients. The overall genovars were distributed as E (41.9%), G (21.6%), F (13.5%), K (9.5%), D (6.8%), J (4.1%), and H (2.7%). CT-positive samples were from males (n = 12, 19.7%), females (n = 42, 68.8%), and anonymous (n = 7, 11.5%) patients, with an age range of 19 to 45 years (average 26.4), including 12 different ethnic groups representative of this region. Most patients were infected with a single genovar (82%), while 18% were co-infected with either two or three genovars. The 1156 bp-fragment of the ompA gene was sequenced in 46 samples to determine single nucleotide polymorphisms (SNP) among isolates. SNP-based subtyping and phylogenetic reconstruction revealed the presence of 13 variants of the ompA gene, such as E (E1, E2, E6), G (G1, G2, G3, G5), F1, K, D (D1, Da2), J1, and H2. Differing genovar distribution was identified among urban (E>G>F) and rural (E>K) populations, and in Slavic (E>G>D) and non-Slavic (E>G>K) ethnic groups. Multilocus sequence typing (MLST) determined five sequences types (STs), such as ST4 (56%, 95% confidence interval, CI, 70.0 to 41.3), ST6 (10%, 95% CI 21.8 to 3.3), ST9 (22%, 95% CI 35.9 to 11.5), ST10 (2%, 95% CI 10.7 to 0.05) and ST38 (10%, 95% CI 21.8 to 3.3). Thus, the most common STs were ST4 and ST9. Conclusion C. trachomatis is a significant cause of morbidity among random heterosexual patients with genital chlamydial infections in the Saratov Region. Further studies should extend this investigation by describing trends in a larger population, both inside and outside of the Saratov Region to clarify some aspects for the actual application of C. trachomatis genotype analysis for disease control.
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